LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units           lj
atom_style      atomic

pair_style      lj/cut 2.5

read_data       data.rigid
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  81 atoms
  read_data CPU = 0.000 seconds

velocity        all create 100.0 4928459

# 1 chain of connected bodies

group           clump1 id <> 1 9
9 atoms in group clump1
group           clump2 id <> 9 18
10 atoms in group clump2
group           clump3 id <> 18 27
10 atoms in group clump3
group           clump4 id <> 27 36
10 atoms in group clump4
group           clump5 id <> 36 45
10 atoms in group clump5
group           clump6 id <> 45 54
10 atoms in group clump6
group           clump7 id <> 54 63
10 atoms in group clump7
group           clump8 id <> 63 72
10 atoms in group clump8
group           clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5                       clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

neigh_modify    exclude group clump1 clump1
neigh_modify    exclude group clump2 clump2
neigh_modify    exclude group clump3 clump3
neigh_modify    exclude group clump4 clump4
neigh_modify    exclude group clump5 clump5
neigh_modify    exclude group clump6 clump6
neigh_modify    exclude group clump7 clump7
neigh_modify    exclude group clump8 clump8
neigh_modify    exclude group clump9 clump9

thermo          100

#dump           1 all atom 50 dump.rigid.poems

#dump           2 all image 100 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    2 pad 5

#dump           3 all movie 100 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    3 pad 5

timestep        0.0001
thermo          50
run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix poems command:

@Article{Mukherjee08,
 author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
 title = {Substructured molecular dynamics using multibody dynamics algorithms},
 journal = {Intl.~J.~Non-linear Mechanics},
 year =    2008,
 volume =  43,
 pages =   {1045--1055}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045742 
     850    17821.483    711.53827            0    3681.7854     7.438428 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19374            0    3681.3037    11.787982 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184716 
    1150    20849.582    206.01696            0    3680.9472  -0.86699118 
    1200    21815.003    45.317409            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064083 
    1300    20780.781    217.36511            0    3680.8286    6.0538604 
    1350    20558.971    254.36489            0    3680.8601   -3.6773868 
    1400    21485.029    99.812844            0    3680.6511   -16.185479 
    1450    21771.107    52.159653            0    3680.6775   -2.4756655 
    1500    21520.949    93.503876            0    3680.3286    2.1023573 
    1550    21351.419     121.6813            0    3680.2511    5.5159876 
    1600    20778.804    216.92191            0    3680.0559    15.089203 
    1650    21477.636    100.21873            0    3679.8247   -1.1045277 
    1700     18501.33     596.4807            0    3680.0357     -15.6798 
    1750     18563.64    587.34824            0    3681.2882    33.532308 
    1800    19110.175    494.82517            0    3679.8543    18.024074 
    1850    21364.178    119.23765            0    3679.9339    2.5290144 
    1900    20146.588    322.15509            0    3679.9197    5.7317299 
    1950    20692.676    231.25264            0    3680.0319     4.297803 
    2000    20943.902    189.11251            0    3679.7629   -22.643824 
    2050    19667.823    401.86882            0    3679.8394    3.6241915 
    2100    20280.125    299.81485            0    3679.8357    7.4804047 
    2150    19181.201     483.6306            0    3680.4975     22.63342 
    2200    21301.144    130.54014            0    3680.7308    4.7074288 
    2250    20484.876    266.98315            0    3681.1291   -8.6578278 
    2300    18648.161    573.07329            0    3681.1001   -5.2550954 
    2350    21515.748    95.243054            0     3681.201    -9.386512 
    2400    21462.551    104.18267            0    3681.2745    -29.46442 
    2450    20107.732    330.99437            0    3682.2831     35.38497 
    2500    20771.509    220.47713            0    3682.3953   -12.324858 
    2550    20499.887    265.58494            0    3682.2327   -22.713874 
    2600    21462.182    105.24427            0    3682.2747   -10.175788 
    2650    21004.949    181.51383            0    3682.3387     4.949195 
    2700    18673.552    570.45017            0    3682.7089    21.201437 
    2750    21257.562      139.198            0    3682.1249   -7.5793039 
    2800    21559.645    88.844759            0     3682.119   -6.2360467 
    2850    20865.227    204.46262            0    3682.0004   0.39575069 
    2900    19428.614    443.93293            0    3682.0352    12.796676 
    2950      19630.1    410.18487            0    3681.8681  -0.50572623 
    3000    19663.218    404.06316            0    3681.2661    6.0827093 
    3050    19087.572     500.8452            0    3682.1073   -6.3526476 
    3100     18229.94    643.77681            0    3682.1001    11.453637 
    3150    18927.492    527.51919            0    3682.1011    -1.662863 
    3200    18320.514    628.55895            0     3681.978    21.176126 
    3250    18204.677    647.96462            0    3682.0775    11.331521 
    3300    19231.978    477.02117            0    3682.3509    3.8381593 
    3350     18153.44    656.70376            0    3682.2772    15.135615 
    3400    17476.768     770.0598            0    3682.8545    -3.394312 
    3450    21097.531    166.17241            0    3682.4276      3.74301 
    3500    17605.784    747.54808            0    3681.8454    3.3420627 
    3550     19238.34    476.00608            0    3682.3961    1.1413836 
    3600    18155.288    656.57434            0    3682.4557    3.4360446 
    3650    18735.622     559.2377            0    3681.8413    28.760363 
    3700    15310.261    1134.4215            0    3686.1317    44.207018 
    3750    15377.116    1123.4786            0    3686.3313    7.6773215 
    3800    18798.895    549.05928            0    3682.2084   -12.905825 
    3850    18322.563    628.87744            0    3682.6379   -16.067793 
    3900    19963.049    355.65441            0    3682.8292    3.4694064 
    3950     19925.48     361.2507            0    3682.1641    5.0058567 
    4000    19141.423    492.41081            0     3682.648   -12.782769 
    4050    20022.241    345.61655            0    3682.6568   -3.0149905 
    4100    21348.635    124.95646            0    3683.0624     -4.85779 
    4150    21011.812     181.1132            0    3683.0819   -3.9526196 
    4200    20222.276    312.63945            0    3683.0187    -23.63437 
    4250    20957.757    189.77152            0     3682.731   -1.3712469 
    4300    20070.215     337.5751            0     3682.611   -6.8816517 
    4350    21322.437    129.09228            0    3682.8318   -6.9442178 
    4400    19440.445    442.77531            0    3682.8495  -0.11606236 
    4450    20964.516    188.67174            0    3682.7577    4.8533525 
    4500     13530.08    1428.5497            0     3683.563    12.333187 
    4550    20461.637    272.58882            0    3682.8616    4.5111943 
    4600    17072.994    836.58228            0    3682.0812    5.7611617 
    4650    18860.748    539.82027            0    3683.2782   -2.5558958 
    4700    18373.927    621.04093            0    3683.3621    5.4020702 
    4750    20321.437    296.63662            0    3683.5428    8.9571617 
    4800    21083.122    169.84086            0    3683.6946    10.566368 
    4850    20499.669     267.7012            0    3684.3128    4.2924237 
    4900    20308.781    300.38168            0    3685.1785   -12.396923 
    4950    21043.303    178.56295            0    3685.7801    3.8923762 
    5000    20718.383    232.52208            0    3685.5859    -12.43234 
    5050    21005.749     184.4363            0    3685.3945   -7.6463487 
    5100    20714.133    233.27745            0    3685.6329   -1.6944135 
    5150    19577.452    422.73035            0     3685.639   -21.831219 
    5200    14044.647    1343.9545            0     3684.729   -6.8407194 
    5250    19089.805     504.0893            0    3685.7235      4.05641 
    5300    21094.745    169.94699            0    3685.7378  -0.66593212 
    5350    19907.559    366.77598            0    3684.7024    1.5248525 
    5400     20382.81    289.13263            0    3686.2676   -11.919321 
    5450    19593.693    420.70548            0    3686.3209   -1.1568628 
    5500     20906.08    202.09801            0    3686.4447   -2.4284971 
    5550    16315.465    965.56973            0    3684.8138   -33.178221 
    5600     19714.57    400.39687            0    3686.1586    19.950231 
    5650    20561.724    259.54797            0     3686.502    8.2074524 
    5700    19349.502     460.7789            0    3685.6959    16.252649 
    5750    21006.818    185.56805            0    3686.7044    -11.96089 
    5800      20268.2    307.97547            0    3686.0089    17.322311 
    5850    21018.322    184.16179            0    3687.2154   -14.379909 
    5900    19695.647    404.57094            0    3687.1787   -20.718904 
    5950    21021.687    183.66311            0    3687.2776   -15.206081 
    6000    18947.535    529.30554            0    3687.2281    17.863927 
    6050    15272.373     1141.012            0    3686.4075  -0.43375666 
    6100    17766.197    721.75792            0    3682.7908    11.378913 
    6150    18612.573    584.06688            0    3686.1623    17.543241 
    6200    19005.155    518.97146            0    3686.4973   -16.223107 
    6250    20997.507    187.55499            0    3687.1394   -11.613546 
    6300    19639.901    413.58048            0    3686.8974    14.407136 
    6350    19580.399    423.02818            0     3686.428   -5.5801796 
    6400    14134.119    1332.0662            0    3687.7527    84.864425 
    6450    21598.824    87.419966            0     3687.224   -5.8358352 
    6500    18208.216    649.29108            0    3683.9938   -8.1510884 
    6550    19364.586    459.59813            0    3687.0291   -12.053563 
    6600    20710.927    235.11914            0    3686.9403   -1.0470193 
    6650    21132.334    165.08091            0    3687.1366    1.0785471 
    6700    20217.285      317.589            0    3687.1365  0.055447462 
    6750    21232.279    148.57412            0    3687.2873   -2.4551657 
    6800    20292.683    304.76539            0    3686.8793  -0.42311295 
    6850    19056.291    510.49927            0    3686.5478    6.9533826 
    6900     20429.82    282.23764            0    3687.2076   -4.2360112 
    6950    21281.278    140.27361            0    3687.1533  -0.07475261 
    7000    17173.388    824.54446            0    3686.7758    10.753828 
    7050      18079.7    674.56274            0     3687.846    12.975804 
    7100    16433.233    950.73904            0    3689.6112     -10.5102 
    7150    19033.335    515.59672            0    3687.8193   0.29109447 
    7200    17286.428    809.02352            0    3690.0948    2.3015698 
    7250    16811.962     886.6645            0    3688.6582   -7.4787512 
    7300    15992.461    1023.4849            0     3688.895   -5.2354222 
    7350    19211.451    487.63129            0    3689.5398    8.4351737 
    7400    19065.682    511.95629            0      3689.57    -12.47448 
    7450    21369.265    128.10098            0    3689.6451    2.2930546 
    7500    16807.109    888.64602            0    3689.8308    14.761969 
    7550    18063.046    679.21873            0    3689.7264    3.8950434 
    7600    17794.987    724.55404            0    3690.3851    14.379016 
    7650    17904.751    706.14354            0    3690.2688    23.813776 
    7700     19670.09     411.3021            0    3689.6504    14.099245 
    7750    18082.562    675.23975            0    3689.0001    15.788521 
    7800    17776.135    726.91445            0    3689.6037    6.9780735 
    7850    17062.575    846.33412            0    3690.0966   -8.9289256 
    7900      19059.2    513.07737            0    3689.6107    16.992843 
    7950    16269.685    978.48914            0    3690.1033    11.180179 
    8000    20115.278    336.91405            0    3689.4604   -6.4882518 
    8050     21173.72    161.15229            0    3690.1056   -2.2164491 
    8100    19238.235    484.42784            0    3690.8004    23.412709 
    8150      18438.4    617.58743            0    3690.6542   0.89156316 
    8200    21438.764    117.12721            0    3690.2546   -1.7193227 
    8250    21195.806    157.66607            0    3690.3003     3.820447 
    8300    21177.549    161.13702            0    3690.7286   0.94938203 
    8350    21060.267    181.06887            0    3691.1135    2.8179025 
    8400    20087.113    343.46206            0    3691.3142    8.1484473 
    8450    19298.478    474.87133            0    3691.2843   -16.239664 
    8500    21654.353    82.083485            0    3691.1423   -8.1464138 
    8550    19920.544    371.34795            0    3691.4386    20.765144 
    8600    21692.293    75.655154            0    3691.0373   -13.316763 
    8650    21231.322     151.8989            0    3690.4526   -11.388238 
    8700    19530.647    434.89585            0    3690.0037    2.7433786 
    8750     19720.63    403.07773            0    3689.8493    -6.416414 
    8800    21321.378    136.04091            0     3689.604    1.3661635 
    8850    19811.906    387.80489            0    3689.7893     3.704143 
    8900    19734.167    400.92444            0    3689.9523    2.5685155 
    8950    21076.459    177.18119            0    3689.9244   -11.939513 
    9000    20967.246    195.42966            0    3689.9707    2.0092705 
    9050    21122.023    169.62103            0    3689.9582    2.3791301 
    9100    20169.346    328.27229            0    3689.8299   -3.5017988 
    9150    21418.641    119.84513            0    3689.6187     2.486073 
    9200    20876.042    210.26452            0    3689.6048   -5.3839897 
    9250     21572.38     93.74407            0    3689.1407   -8.3676952 
    9300     20944.78    197.98577            0    3688.7824    1.3278314 
    9350     20706.52    237.48767            0    3688.5744    4.6944204 
    9400    16412.314    953.47251            0    3688.8581    26.134976 
    9450     20461.68    277.76243            0    3688.0424    17.647445 
    9500    20893.994    205.64261            0    3687.9749   -10.642418 
    9550    20503.447    270.63504            0    3687.8761   -17.769897 
    9600    19677.799    408.05887            0     3687.692   -2.7938604 
    9650    17480.971     774.1855            0    3687.6806   0.59827043 
    9700    17799.126    721.50817            0    3688.0292    44.387928 
    9750    20443.384    280.16837            0     3687.399    3.0619324 
    9800    20545.255    263.40108            0    3687.6102    3.6229381 
    9850    20722.819    233.57142            0    3687.3745   0.86462694 
    9900    21128.462    165.09767            0     3686.508   -6.9636843 
    9950    21343.307    130.46714            0     3687.685   -9.7382705 
   10000    20623.887    250.37866            0    3687.6932    2.7529835 
Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms

Performance: 38035.351 tau/day, 4402.240 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.092926   | 0.092926   | 0.092926   |   0.0 |  4.09
Neigh   | 0.076362   | 0.076362   | 0.076362   |   0.0 |  3.36
Comm    | 0.0069691  | 0.0069691  | 0.0069691  |   0.0 |  0.31
Output  | 0.0037444  | 0.0037444  | 0.0037444  |   0.0 |  0.16
Modify  | 2.0832     | 2.0832     | 2.0832     |   0.0 | 91.71
Other   |            | 0.00841    |            |       |  0.37

Nlocal:             81 ave          81 max          81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             62 ave          62 max          62 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            905 ave         905 max         905 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 905
Ave neighs/atom = 11.17284
Neighbor list builds = 991
Dangerous builds = 927
Total wall time: 0:00:02
